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- PDB-1i37: CRYSTAL STRUCTURE OF THE RAT ANDROGEN RECEPTOR LIGAND BINDING DOM... -

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Basic information

Entry
Database: PDB / ID: 1i37
TitleCRYSTAL STRUCTURE OF THE RAT ANDROGEN RECEPTOR LIGAND BINDING DOMAIN COMPLEX WITH DIHYDROTESTOSTERONE
ComponentsANDROGEN RECEPTOR
KeywordsHORMONE/GROWTH FACTOR / ANDROGEN RECEPTOR / STEROID RECEPTOR / NUCLEAR RECEPTOR / TRANSCRIPTION REGULATION / LIGAND-BINDING DOMAIN / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


reproductive behavior / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / copulation / male sex differentiation / skeletal muscle hypertrophy / regulation of prostatic bud formation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / male courtship behavior / positive regulation of penile erection / ribonucleotide binding ...reproductive behavior / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / copulation / male sex differentiation / skeletal muscle hypertrophy / regulation of prostatic bud formation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / male courtship behavior / positive regulation of penile erection / ribonucleotide binding / Ub-specific processing proteases / male somatic sex determination / : / lateral sprouting involved in mammary gland duct morphogenesis / SUMOylation of intracellular receptors / reproductive system development / POU domain binding / negative regulation of integrin biosynthetic process / regulation of developmental growth / reproductive structure development / male genitalia morphogenesis / positive regulation of integrin biosynthetic process / Nuclear Receptor transcription pathway / intracellular receptor signaling pathway / tertiary branching involved in mammary gland duct morphogenesis / animal organ formation / androgen binding / cellular response to follicle-stimulating hormone stimulus / Leydig cell differentiation / regulation of systemic arterial blood pressure / epithelial cell morphogenesis / prostate gland growth / epithelial cell differentiation involved in prostate gland development / positive regulation of epithelial cell proliferation involved in prostate gland development / membraneless organelle assembly / prostate gland epithelium morphogenesis / cellular response to testosterone stimulus / fertilization / RNA polymerase II general transcription initiation factor binding / positive regulation of insulin-like growth factor receptor signaling pathway / positive regulation of intracellular estrogen receptor signaling pathway / positive regulation of transcription by RNA polymerase III / nuclear androgen receptor binding / cellular response to steroid hormone stimulus / morphogenesis of an epithelial fold / seminiferous tubule development / androgen receptor signaling pathway / response to testosterone / single fertilization / mammary gland alveolus development / regulation of protein localization to plasma membrane / cellular response to estrogen stimulus / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / positive regulation of phosphorylation / estrogen receptor signaling pathway / steroid binding / insulin-like growth factor receptor signaling pathway / epithelial cell proliferation / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of cell differentiation / molecular condensate scaffold activity / response to insulin / multicellular organism growth / transcription coactivator binding / positive regulation of miRNA transcription / beta-catenin binding / nuclear receptor activity / male gonad development / negative regulation of epithelial cell proliferation / MAPK cascade / response to estradiol / positive regulation of NF-kappaB transcription factor activity / ATPase binding / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / in utero embryonic development / sequence-specific DNA binding / transcription by RNA polymerase II / positive regulation of MAPK cascade / molecular adaptor activity / transcription cis-regulatory region binding / nuclear speck / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / protein domain specific binding / axon / signaling receptor binding / negative regulation of DNA-templated transcription / dendrite / chromatin binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription
Similarity search - Function
Androgen receptor / Androgen receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors ...Androgen receptor / Androgen receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
5-ALPHA-DIHYDROTESTOSTERONE / Androgen receptor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSack, J.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Crystallographic structures of the ligand-binding domains of the androgen receptor and its T877A mutant complexed with the natural agonist dihydrotestosterone.
Authors: Sack, J.S. / Kish, K.F. / Wang, C. / Attar, R.M. / Kiefer, S.E. / An, Y. / Wu, G.Y. / Scheffler, J.E. / Salvati, M.E. / Krystek Jr., S.R. / Weinmann, R. / Einspahr, H.M.
History
DepositionFeb 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANDROGEN RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5732
Polymers30,2821
Non-polymers2901
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.080, 65.760, 70.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ANDROGEN RECEPTOR / DIHYDROTESTOSTERONE RECEPTOR


Mass: 30282.414 Da / Num. of mol.: 1 / Fragment: LIGAND-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PET28B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P15207
#2: Chemical ChemComp-DHT / 5-ALPHA-DIHYDROTESTOSTERONE


Mass: 290.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H30O2 / Comment: hormone*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.88 M NA TARTRATE, 0.1M NA HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal grow
*PLUS
Temperature: 20 ℃
Details: drop consists of equal amounts of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 mg/mlprotein1drop
20.8 MNa, K tartrate1reservoir
30.1 MNa HEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: BRUKER / Detector: CCD / Date: Jun 17, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 17329 / % possible obs: 94.8 % / Redundancy: 7.3 % / Biso Wilson estimate: 29.3 Å2 / Rsym value: 0.101 / Net I/σ(I): 12
Reflection shellResolution: 2→2.1 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 4 / Rsym value: 0.256 / % possible all: 73
Reflection
*PLUS
Rmerge(I) obs: 0.101
Reflection shell
*PLUS
% possible obs: 73 % / Rmerge(I) obs: 0.256

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Processing

Software
NameClassification
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A28

1a28


Resolution: 2→10 Å / Data cutoff high absF: 999999 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 2
Details: The side chains of residues 845-850 were not seen in the density. HIS-TAG (RESIDUES 664 TO 671) AND RESIDUES 918 TO 919 WERE NOT SEEN IN THE ELECTRON DENSITY AND ARE PRESUMED TO BE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.312 743 4.9 %RANDOM
Rwork0.242 ---
obs-15067 82.6 %-
Displacement parametersBiso mean: 25.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1990 0 21 106 2117
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.014
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg1.6
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d21.5
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d1.56
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.367 52 4.9 %
Rwork0.302 1058 -
obs--76.8 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.56
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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